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- PDB-9bjr: X-ray crystal structure of Y168F variant Thermothelomyces thermop... -

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Basic information

Entry
Database: PDB / ID: 9bjr
TitleX-ray crystal structure of Y168F variant Thermothelomyces thermophilus polysaccharide monooxygenase 9E
ComponentsGlycoside hydrolase family 61 protein
KeywordsOXIDOREDUCTASE / polysaccharide monooxygenase
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / hydrolase activity / extracellular region / metal ion binding
Similarity search - Function
Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / OXYGEN MOLECULE / lytic cellulose monooxygenase (C4-dehydrogenating)
Similarity search - Component
Biological speciesThermothelomyces thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThomas, W.C. / Sayler, R.I. / Marletta, M.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM143897 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM149060 United States
National Science Foundation (NSF, United States)CHE-1904540 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Electron transfer in polysaccharide monooxygenase catalysis.
Authors: Sayler, R.I. / Thomas, W.C. / Rose, A.J. / Marletta, M.A.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 61 protein
B: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,06211
Polymers48,5642
Non-polymers4989
Water6,251347
1
A: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5616
Polymers24,2821
Non-polymers2795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5025
Polymers24,2821
Non-polymers2204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.989, 119.970, 92.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase family 61 protein / Lytic polysaccharide monooxygenase


Mass: 24281.832 Da / Num. of mol.: 2 / Mutation: Y168F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces thermophilus (fungus) / Gene: MYCTH_79765 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD 1163 / References: UniProt: G2Q7A5

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Non-polymers , 5 types, 356 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.95 % / Description: Plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The crystal was grown by hanging drop in conditions optimized from Hampton Index HT G8 (0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 35 % w/v polyethylene glycol 3,350). 1 ul 30 mg/mL Mt ...Details: The crystal was grown by hanging drop in conditions optimized from Hampton Index HT G8 (0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 35 % w/v polyethylene glycol 3,350). 1 ul 30 mg/mL Mt PMO9E in 50 mM MOPS, 50 mM MES was mixed with 1 uL with 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, and 35% PEG 3,350. The crystal was then cryoprotected for 10 seconds in well solution mixed with cryoprotectants to a final concentration of 8% w/v sucrose, 2% w/v glucose, 8% v/v glycerol, and 8% ethylene glycol
PH range: 7-7.5 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.2→58.62 Å / Num. obs: 27208 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.992 / CC star: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.057 / Rrim(I) all: 0.113 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2376 / CC1/2: 0.843 / CC star: 0.963 / Rpim(I) all: 0.211 / Rrim(I) all: 0.407 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→58.62 Å / SU ML: 0.2442 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2128 2000 7.36 %
Rwork0.1749 25189 -
obs0.1777 27189 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→58.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 26 347 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383565
X-RAY DIFFRACTIONf_angle_d0.64984867
X-RAY DIFFRACTIONf_chiral_restr0.0474518
X-RAY DIFFRACTIONf_plane_restr0.0044659
X-RAY DIFFRACTIONf_dihedral_angle_d12.86751254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.28551440.22881805X-RAY DIFFRACTION99.14
2.26-2.320.28361420.22521803X-RAY DIFFRACTION98.88
2.32-2.380.27321440.21211811X-RAY DIFFRACTION99.24
2.38-2.460.30271430.21681790X-RAY DIFFRACTION98.82
2.46-2.550.26221430.21041813X-RAY DIFFRACTION98.64
2.55-2.650.27971440.20531815X-RAY DIFFRACTION98.39
2.65-2.770.2411440.20021801X-RAY DIFFRACTION98.03
2.77-2.920.26081390.19911756X-RAY DIFFRACTION96.05
2.92-3.10.22221370.18691725X-RAY DIFFRACTION93.33
3.1-3.340.21411440.18341813X-RAY DIFFRACTION97.51
3.34-3.680.20271430.16931805X-RAY DIFFRACTION97.74
3.68-4.210.17571430.14791798X-RAY DIFFRACTION96.81
4.21-5.30.14381440.1181811X-RAY DIFFRACTION95.69
5.3-58.620.14211460.14471843X-RAY DIFFRACTION93.42

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